Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

[FreeSurfer] Importing DICOM Files
by Matthew Clem 11 Jul '14

11 Jul '14

Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 0000142 \ -i $SUBJECTS_DIR/0000142/000001.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/0000142/000001.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0000142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center Matthew.Clem(a)utsouthwestern.edu<mailto:tabatha.melton@utsouthwestern.edu> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Tutorial Installation Issue
by Kundrod, Kathryn (NIH/NIBIB) [F] 11 Jul '14

11 Jul '14

Hi all, I have a question regarding the installation of the buckner tutorial dataset. I have been able to download and unzip the tutorial data, but it seems only partially downloaded. In the readme, I see that there are supposed to be 3 subfolders to the dataset: group_study, tutorial_subjs, and raw, but my download only contains one subfolder (tutorial_subjs). I have tried downloading multiple times in multiple ways without a change in results. Is anyone aware of what might be causing this? Thank you! Kathryn Kundrod

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exporting movies from freeview
by pavitrak＠nmr.mgh.harvard.edu 11 Jul '14

11 Jul '14

Hi Freesurfer Team, I have a 4D volume mask of MRI mask values over time - which I can view frame by frame within Freeview. Is there any way to export this in movie form out of freeview so I can play it back independently of the interface? Thank you. Best Regards, Pavitra

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Correlation coeffecient
by Chris Wertz 11 Jul '14

11 Jul '14

Hi Freesurfer experts I am trying to obtain correlation coefficients for significant clusters and found a previous post about this, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html but the MATLAB function link within this post is dead? any help is greatly appreciated thanks, Chris

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create label from binary .mgh file
by Lars M. Rimol 11 Jul '14

11 Jul '14

Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Creating own atlas
by Brianna Damadian 11 Jul '14

11 Jul '14

Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna

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Anterior Temporal Lobe / Pial Reconstruction Troubles - part 2
by Las Blawimo 11 Jul '14

11 Jul '14

Attached you will find image 3 and 4. Sincerely, Las

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Convert label file to STL file‏
by Mat yuki 10 Jul '14

10 Jul '14

Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just check how mris_convert works). Second, I copied lh. white file from surf dir into label dir. Then, I runed next command: cd <subjid>/label mris_convert --label lh.bankssts.label bankssts lh.white lh.bankssts.label.stl And got the error message: ERROR: unknown file annot file type specified for output: lh.bankssts.label.stl Do you know what could have gone wrong? Thank you, Yuki.

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ACPC alignment in freeview?
by Tracy Riggins 10 Jul '14

10 Jul '14

Hello Freesurfer experts: I am wondering if I can do ACPC alignment in freeview. Perhaps using Tools> Transform volume and then rotating using landmarks. Is this indeed possible? If so, can anyone provide guidance on the 3 landmarks to select (would it be anterior commissure superior & posterior edges & posterior commissure) and how to map these landmarks to coordinate axis vectors? I would appreciate it. Thanks in advance, Tracy Riggins

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Save automatically masks drawn in Freeview
by Dorian P. 10 Jul '14

10 Jul '14

Hi users and developers, I am currently using Freeview to draw about 25 masks per subject for 60+ subjects. After generating the volume in Freeview, giving them the proper name, and drawing the ROI, I need to save them one by one, giving also the extension .nii to have the file as niftii. This procedure is very time consuming and prone to errors (filenames need to be precise). Is there a way to save the generated masks automatically, perhaps by selecting the volumes all at once, pressing save, and the software automatically saves them with the same name given in Freeview and with the extension .nii? Any suggestion is welcome, even if it requires hacking the software somewhere... Using Ubuntu 12.04 and Freesurfer 5.0.3. Thank you. Dorian TJU

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