Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Selecting OS for image analysis
by Ramesh Babu 24 Oct '17

24 Oct '17

Dear Experts, I have purchased a new pc. I want to use for MRI and EEG analysis by using MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these software? I have NVIDIA graphics card 610 in my system. I am using Ubuntu in another systm and little bit of experience in cent os. Thank in advance Ramesh

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surface based correlation analysis
by John Anderson 24 Oct '17

24 Oct '17

Dear Dr Doug, I want to study the relationship between PET signal measured as the mean signal of the whole cortex and gray matter volume to find regions of association between gray matter atrophy and PET signal. In this case I will need to run surface based analysis and the FSGD file must be "One Group, One Covariate" is this correct? Thanks for any suggestions/ advice! John

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Re: [Freesurfer] segmentHA znzread failed error
by Iglesias Gonzalez, Eugenio 24 Oct '17

24 Oct '17

Wow never seen that before. Does the output look OK? (segmentation and volumes) Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 24 October 2017 at 14:31 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA znzread failed error Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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aparcstats2table surface area
by Kasper Jessen 24 Oct '17

24 Oct '17

Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1. The ROIs extracted are by default the White Surface Area, correct? 2. Why does the WhiteSurfArea (default average) have decimals but not the surface area of the different ROIs? When taking the SUM of all the ROIs, it does not equal the WhiteSurfArea and I am thinking this must be due to the decimals? Best Regards Kasper ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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segmentHA znzread failed error
by Maksimovskiy, Arkadiy 24 Oct '17

24 Oct '17

Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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[job] Program Manager for the Brain Imaging Data Structure project
by Chris Gorgolewski 23 Oct '17

23 Oct '17

Do you have great people skills and enjoy organizing events? Are you interested in helping neuroscientists exchange data in a more useful way? The Brain Imaging Data Structure project is looking for a full time Program Manager - this might be a perfect job for you! No neuroimaging experience is required, but some will come handy. This position might be especially attractive if you appreciate working in an academic environment, but prefer to avoid the stress of “publish or perish” and enjoy a competitive salary. The position is based in the legendarily sunny San Francisco Bay Area. The successful candidate will receive relocation support. More details at https://stanford.taleo.net/careersection/2/jobdetail.ftl?job=76713&lang=en#…. We will start reviewing applications on the 6th of November. Best regards, Chris Gorgolewski PS Apologies for cross posting - please forward this ad if you know someone who might be interested.

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Tracula --- Volume and path length are equal
by Mehta, Chintan 23 Oct '17

23 Oct '17

Dear FreeSurfer users, I am using FreeSurfer 6.0 and Tracula 6.0. For many subjects that I'm processing, the volume and path length are equal to each other. For ~60% of subjects, the "pathstats.overall.txt" file shows something like: Count 1500 Volume 34 Len_Min 34 Len_Max 34 Len_Avg 34 Len_Center 34 AD_Avg 0.00104677 AD_Avg_Weight 0.00104677 AD_Avg_Center 0.00104677 RD_Avg 0.000594649 RD_Avg_Weight 0.000594649 RD_Avg_Center 0.000594649 MD_Avg 0.000745357 MD_Avg_Weight 0.000745357 MD_Avg_Center 0.000745357 FA_Avg 0.364984 FA_Avg_Weight 0.364984 FA_Avg_Center 0.364984 This output suggests that only a single pathway was computed for a subject with output like above (since Len_Min = Len_Max = Len_Avg = Len_Center); yet the count number suggests that 1,500 paths were generated. This obviously seems problematic. I have two questions: 1) Does the problem originate during the fitting of the ball-and-stick models at each voxel? (I used n=3 sticks with bedpostx). If so, how can I rerun this process to ensure this problem does not repeat? 2) Is it possible that each probabilistic track was generated with the same random seed? If so, would this problem be associated with the ball-and-stick model step (with bedpostx_gpu) or pathway fitting step (-path)? 3) Are the anisotropy measures (such as FA_Avg, MD_Avg_Weight, etc) independent of this problem? Or do they also require different probabilistic paths be generated? I suspect this issue may have arisen due to my using "bedpostx_gpu" to fit the ball-and-stick models (default setting). Thank you much in advance. Best, Chintan

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Help with extraction of cortical thickness from ROI and creation of mask.
by Dennis M. Hedderich 23 Oct '17

23 Oct '17

Dear Freesurfer Team, I built a GLM, did a 2 sample t-test and found significant differences in cortical thickness in the right middle temporal gyrus between two groups. Now, I would like to kindly ask for your help with two problems that I am facing: 1) for further correlation analyses in SPSS, I would like to extract cortical thickness exactly from the region of difference in the middle temporal gyrus of every subject. Extraction of cortical thickness of the whole middle temporal gyrus worked well, however there is a lot of noise in that information because the area of significant difference is a lot smaller than the MTG roi from the Desikan atlas. 2) to assess thalamocortical structural connectivity to that region, I would like to create and extract a mask in MNI space that I could use with fsl. Is that possible? Thank you very much in advance for any kind of help. Best wishes, Dennis

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Wm edits and wm surface
by Maksimovskiy, Arkadiy 22 Oct '17

22 Oct '17

Hi Everyone, I looked through archived messages, and even though this was mentioned, I did not quiet find a clear response. Is it necessary to make edits to the wm volume if the wm surface is accurate? For example, if the surface follows the wm boundary accurately, but the wm volume has 1. some extra voxels filled outside of the brain or 2. Wm has some voxels not filled inside of it. Any information would be greatly appreciated. Thanks, Arkadiy

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apply transformation using talairach.m3z
by Gidon Levakov 22 Oct '17

22 Oct '17

Hi Freesurfer experts, I have several nifti images (created with another software) in the subjects original anatomical space (native space) that I want to transform to a common space (freesurfer version of MNI305 should be fine) using non-linear transformation. Reading a previous answer regarding this issue ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03355…) I understand I should use the *mri_vol2vol* command to apply the transformation stored in the file *mri/transforms/talairach.m3z* (I already run recon all). But after checking the result, the images are still not align with each other and do not resemble the *mni305.cor.mgz* file. I used the following command: mri_vol2vol --m3z my_subjects_dir/sub_X/mri/transforms/talairach.m3z --noDefM3zPath --reg_header --mov file_loc/img.nii.gz --targ /usr/local/freesurfer/average/mni305.cor.mgz --o file_loc/img_warped.nii.gz I also tried without the --reg_header option with no success. Any idea what I am doing wrong? can you give me an example that works? Thanks in advance! Gidon l.

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Freesurfer October 2017