[Freesurfer] TRACHEAL error

Hello Freesurfers!I’m trying to use tracheal -prep, and I’m getting an error. Would you please help me with figuring out where the problem is? The log file is attached.Thank you very much,EmadEmad Ahmadi, MD---Research FellowDepartment of RadiologyMassach

Re: [Freesurfer] TRACHEAL error

* I’m trying to use trac-all > On Mar 4, 2015, at 4:42 PM, Emad Ahmadi wrote: > > Hello Freesurfers! > > I’m trying to use tracheal -prep, and I’m getting an error. Would you please > help me with figuring out where the problem is? The log file is attached. > > Tha

Re: [Freesurfer] Trac-all error

lib/libGLU.1.dylib > > Does the freesurfer build that you're using match the computer that you're > running it on? > > a.y > > On Wed, 4 Mar 2015, Emad Ahmadi wrote: > >> Hello Freesurfers! >> >> I’m trying to use tracheal -prep, and I’m gett

Re: [Freesurfer] Trac-all error

:11 PM, Anastasia Yendiki >>> mailto:ayend...@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> Hi Emad - The error is: >>> dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib >>> >>> Does the freesurfer build that you're using match the

[Freesurfer] Recon-all error

Hi,I keep getting an error when I run recon-all and can’t figure out what is wrong. I would really appreciate your help. I’ve attached the log file.Thank you so much,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General

[Freesurfer] Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?

like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 72

[Freesurfer] Do these bvec and bval files match?

Hello, I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and I'm using dcm2niigui app to generate bvec and bval files from DICOMs. My question is whether or not the attached bvec and bval files match, because the 0 bval is the first entry while the <0,0,0> bvec is somewhere i

[Freesurfer] Generating list of subjects: a tcsh scripting problem

Hello, I am having a tcsh scripting problem for generating a text file containing the list of subjects, and I would appreciate any help. I've explained my problem here: http://stackoverflow.com/q/20617206/2769441 All the best, Emad ___ Freesurfer maili

[Freesurfer] Recon-all exits with errors for a patient with TBI

Hello, I'm analyzing some images of patients with TBI. There's one of them having abnormalities in T1 images (skull fracture, epidural/intracranial hemorrhage, shifts) that can trouble image registration; when I run recon-all for this patient, it exits with errors. I wonder if it has anything to d

[Freesurfer] recon-all error

Hello & Happy New Year! I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached. All the best throughout 2014! Emad Emad A

[Freesurfer] Recon-all error

ally go through the analysis pipeline, but it gives me the error and exits. Thank you very much, Emad Emad Ahmadi, MD Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite

[Freesurfer] How to clone from T1 to brainmask in freeview to amend a bad skull strip

Hi! I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend a skullstript that has removed too much). I couldn’t find the tool in freeview. Thank you very much, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of

[Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView

Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology

Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView

in >> new subjects? If the latter it requires manually labeling a training set and >> rebuilding a classifer, etc..., so it is far from trivial >> >> cheers >> Bruce >> >> >> On Mon, 3 Mar 2014, Emad Ahmadi wrote: >> >>> Hello, >>>

[Freesurfer] Applying a precomputed transform matrix to an image in free surfer

, Emad P.S. I know that for this particular example, I can use the anatomical images in dlabel/diff, but the point for me is to learn how to apply a transform matrix to an image and generate a transformed image in freesurfer Emad Ahmadi, MD --- Postdoc

[Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

-exported dicoms back to Launchpad 5. Run dcm2niix on the new dicoms Since this copying back and forth takes a lot of time, I need a better way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! I would really appreciate your help. Best, Emad Emad Ahmadi, MD

Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

/ > then run dcm2nii. > With that I have no problems. > > hth > d > > On 10/30/15 10:28 AM, Emad Ahmadi wrote: >> Hi Freesurfer experts, >> >> I hope you’re all enjoying your day! >> >> Working in Launchpad, I want to extract the bvals/bvecs

[Freesurfer] Free surfer dev env doesn't extract bvals/bvecs

file. I would appreciate your help!Best,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu

[Freesurfer] Is the x-component of the b vectors extracted by mri_convert inverted?

onfirm that I should invert the x-component of the bvecs extracted via mri_convert (I had the same experience with dcm2nii tool, where I had to invert the z-component of the extracted bvecs). I hope a wonderful new year for everyone! Emad Emad Ahma

[Freesurfer] Longitudinal TRACULA - Error in path reconstruction

at I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Cha

[Freesurfer] Unpacking Problem

Hello,I’m trying to unpack and run recon-all on a set of MEMPRAGE images we’ve obtained in Lunder 6 scanner (Siemens Skyra), but recon-all is giving me errors. I’ve attached for the scan.info file (outputted by unpacksdcmdir), the unpack.config file that I used to unpack the MEMPRAGE images, and th

[Freesurfer] Dura correction using MEMPRAGE vs bandwidth-matched FLAIR

into recon-all for dura correction, or if we should leave the T2-SPACE-FLAIR sequence as it is and use the four echoes of MEMPRAGE for dura correction (I mean, is dura correction using different echoes of MEMPRAGE as good as feeding FLAIR images into recon-all?)Thank you very much,Emad Emad Ahmadi

Re: [Freesurfer] Recon-all error

is ok, and also > monitor memory usage. It died right in the middle of mri_ca_label which I > can't remember seeing before > > > On Mon, 7 Jul 2014, Emad Ahmadi wrote: > >> Hello FreeSurfers, >> >> Wish you a great summer time! >> >> I’m