Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

Quantifying volumes
by Josue Luiz Dalboni Da Rocha 12 Oct '16

12 Oct '16

Dear Douglas, I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus. I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file. Can I extract statistics directly from the ".curv" file? Or can I convert directly from .curv to .label in order to extract these statistics? As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)? What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space? Thank you very much in advance for your help! Best regards, Josue

3 7

Segmentation editing
by firetech＠web.de 12 Oct '16

12 Oct '16

2 1

Fw: freeview: command not found
by Mageshwar Selvakumar 12 Oct '16

12 Oct '16

Dear All, I'm trying to start on with freeSurfer. I have a Mac running Mac OS Sierra. I downloaded the file "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwi…>" and installed it. I have setup the license file and also configured free surfer. Once I tried running the examples provided to check the software, the first example ran without errors but the second example that uses Freeview returned a error: command not found. On looking for a solution in the archives, I found someone had a similar problem using tkmedit, Freeview on a linux machine. When I tried tkmedit it works without errors, giving a long list of commands it supports. So, the problem command not found is only when I use Freeview. I also tried using only the freeview command and still the error remained. Kindly let me know if someone had a similar problem, or if someone is running free surfer successfully on Mac OS Sierra. PS: I had given read and write rights to the entire free surfer folder as well. Thank you for your help. Kind Regards Mageshwar Selvakumar

1 0

Use Atlas (Binary ROIs) made in 3DSlicer in as parcellation atlas in Freesurfer
by Daya P 11 Oct '16

11 Oct '16

Hi All, We made an average subject for a non-human species and made ROI in nifiti format in Slicer, it's basically an atlas were each region corresponds to a different number. My question is if there is any way to import this into Freesurfer and be able to use this as any other parcellation atlas that comes with Freesurfer? What would be the process for that? Thank you, Daiana

1 0

Volume to Surface
by Crawford, Anna 11 Oct '16

11 Oct '16

Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

4 27

FreeSurfer 6 beta and mac osx el capitan
by Damien MARIE 11 Oct '16

11 Oct '16

Hi, I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El capitan 10.11.6, XQuartz 2.7.9 installed). I allowed applications downloaded from Anywhere in privacy and settings, and disabled csrutil (the System Integrity Protection, a security feature that hobbles some of the capabilities of root since this OS release). No matter what I try, I cannot decompress the archive. Using the terminal and sudo : tar: Error opening archive: Failed to open '/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’ Or by double clicking : Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not permitted). I was wondering if somebody experienced this issue and would eventually have a solution. Thank you and best, Damien

1 1

Subcortical segmentation
by Ankita Sharma 10 Oct '16

10 Oct '16

Hi, Does anyone know if subthalamic nuclei and substantial nigra are part of the automated sub-cortical segmentation (aseg) in Freesufer? Thanks, Ankita!

2 1

Subcortical Segmentation
by Raghav Mehta 10 Oct '16

10 Oct '16

Hi, I am new to freesurfer. I would like to know the command for subcortical segmentation of brain MRI volume. I read on freesurfer wiki page the recon-all -autorecon2 stage is useful for this. *My question is what exact command should I use for this purpose.* I am familiar with FSL. In FSL 'FIRST' command is useful for this and it gives you segmentaion in approimately 7-10 minutes. But in freesurfer it is written that recon-all -autorecon2 stage can take upto 12 hours for segmentation of one volume. I would like to know if there is any other option for this apart from autorecon2 stage which can give me segmentation in less time. Thank you for your help. Regards, Raghav Mehta MS by Research (ECE) Center for Visual Information Technology International Institute of Information Technology - Hyderabad +91 9712990393

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qdec long parsing table to look in non-existant directory
by Katherine Damme 09 Oct '16

09 Oct '16

Hello everyone, I am running qdec for longitudinal data for the first time and although I have a file that matches the guide on the wiki, the script is looking in a non-exsistant file location (see below). While there is a 1001 file and a 1001_MR1, I am not sure where it is getting the 1001_MR1.long.1001 dir. Any ideas? "long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-stack --do-label --time years --qcache fsaverage --sd /home/adapt/Cortical_Thickness_Data Parsing the qdec table: long.qdec.table.dat Working in SUBJECTS_DIR: /home/adapt/Cortical_Thickness_Data Working on hemi: lh Subject-Template: 1001 INFO: 2 TPs in 1001 , mean age: 0.487704918 =============================================================================== SUBJECT 1001 Intersecting Within-Subject Cortex Label ERROR: /home/adapt/Cortical_Thickness_Data/1001_MR1.long.1001/label/lh.cortex.label does not exist!"

2 1

QAtools - tkmedit and detailed snapshots all black
by Sneha Pandya 07 Oct '16

07 Oct '16

Dear experts, I am running QA tool on our current recon runs and am getting black image for all tkmedit and detailed snapshots. While running the tool, tkmedit window pops up and everything looks fine. Per instruction I am making sure that no other interactive window is open. Even otherwise when I take screen shot from within tkmedit window using screen shot button, it is still black. Please see QA tool summary . Can anyone advice what is wrong? [cid:bef1900c-65af-44e4-85fe-3a26322c7a23] Thanks, Sneha

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