Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

Creating functional ROI
by Ashley Cole 13 Dec '17

13 Dec '17

Dear Doug/Bruce, I appreciate any insights on this. Thank you, Ashely ------------------------------------ I am new to FreeSurfer and I apologize in advance if my questions are too naiive. My main goal is to keep everything in the native space. Also, I am looking for percent signal change in selected ROIs. First, I ran recon-all command. Then, I preprocessed the functional data in native space. The command that I ran was: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force Then, I configured my analyses and contrasts in each hemisphere, as well as the volume. Finally, I ran the analyses for each hemispheres and the volume. I ran this command: selxavg3-sess -s sess01 -analysis ffa.native.rh Lastly, I visualized the results by running these commands: tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies -self tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self So far, I think I have done everything correctly. I am seeing the activation ROIs where I am supposed to. Now, I would like to be able to select these ROIs/clusters, take their voxel coordinates/numbers and create a mask. (These are my localizer nii files.) Then, use this mask on the main experiment (non localizer) nii files and get the percent signal change in those selected voxels. Is this possible? I have found this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/ CreatingROIs but unfortunately I am not following it. I don't see these options in tksurfer. Also is it possible to create an ROI on the surface? I appreciate any help. Thank you so much Ashley Cole

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Hippocampal Subfield and Amyg Nuclei ICV Correction
by Maksimovskiy, Arkadiy 13 Dec '17

13 Dec '17

Dear Experts, I have seen this question pop up a few times in the forum, but have not seen a clear response, so I was wondering if someone might be able to clarify or offer their opinion. 1. Do the hippocampal subfields and amygdala nuclei need to be corrected for ICV (either by including ICV as a covariate or taking the ration if each subfield to the ICV)? 2. If so, might it make more sense to correct them (perhaps take the ratio of each subfield to the hippocampus) for the volume of the hippocampus (after the hipp. itself has been corrected for the ICV)? If the correction is recommended, I am wondering about whether the second option might be better, because the ICV correction might be introducing too much variability for such a small sub-structure, whereas, correcting for just the hippocampus volume might be a bit more accurate. I found two ways of dealing with this in the relevant papers for the hipp. Subfield and amyg nuclei, respectively, quoted below: “Then, we correct these estimates for age and intracranial volume (ICV) by regressing them out with a general linear model. This step is important because the subregion volumes are strongly correlated with these two variables, which can easily confound the analysis – subjects with large ICV and/or of younger age are expected to have larger hippocampi; see for instance (Mueller, Schuff, Yaffe, Madison, Miller, & Weiner, 2010). Moreover, such correction was used in (Mueller, et al., 2013), so we used this correction as well in order to directly compare the results” (Iglesias, 2015) “ICV was added as a covariate to all ANOVAs” (Saygin, 2017) I would love to hear any advice/perspective. Thank you in advance. Arkadiy

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cortical thickness smoothing
by John Anderson 13 Dec '17

13 Dec '17

Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths": fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float I want to smooth two different modality-images using the cortical thickness smoothing method. Thank you for any advice! John

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[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 13 Dec '17

13 Dec '17

Hi Andrew, Thanks very much! I have tried the new version of make_average_surface and it works fine. I am very gratefull. Best, M del Mar

1 0

Research engineer in Neuroimaging wanted
by Olivier Coulon 13 Dec '17

13 Dec '17

Dear Freesurfer list, the 'Institut de Neuroscience de la Timone <http://int.univ-amu.fr>' (INT), Marseille, France, is looking for a research engineer for a duration of one year. The candidate will bring a scientific support to MR neuroimaging research. If satisfactory, the contract will lead to a permanent position as an Aix-Marseille University research engineer at INT. Do not hesitate to pass this annoucement to anybody interested. Full details are available following this link <https://amubox.univ-amu.fr:443/index.php/s/pUDtyMjJEI2VoxP>. contact: olivier.coulon(a)univ-amu.fr -- Olivier Coulon, CNRS Research Director Aix-Marseille University, Institut de Neurosciences de la Timone Faculté de Médecine, 27 Bd Jean Moulin 13005 Marseille - France MeCA Research Group http://www.meca-brain.org https://sites.google.com/site/oliviercoulon olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univ-amu.fr> Tel: +33 (0)4 91 32 40 59

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Cortical thickness clarification
by Rockers, Elijah D. 12 Dec '17

12 Dec '17

Hello, I was hoping to get some clarification on how exactly the cortical thickness number is calculated. In the videos, Doug says it's "the distance between the vertex on the white to the vertex on the pial, and you go backwards and forwards to compute the average thickness", and the 2000 paper says "the thickness is computed as the average of this distance measured from each surface to the other". From what I understand, You find the closest vertex on the pial surface from a given white matter surface vertex, then calculate the distance both ways and take the average. Why is the value not the same both ways, i.e., from white to pial, and from pial to white? Thanks very much, Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Qdec Table Loading Error
by Arsenije Subotic 12 Dec '17

12 Dec '17

Dear experts, I'm currently trying to import some of my data into Qdec in order to perform a group analysis on cortical thickness. All of my data was originally in an excel sheet and it had the following variables (fsid, gender, age, and thickness). I tried converting it into a file that would be opened with Qdec. I use a mac and I originally tried to export the file into text editor and I tried saving it as "qdec.table.dat", which had no problems being opened in text edit. However, when I tried loading it into qdec it gives me an error:"error loading the data table". I'm quite new to Qdec (this is my first week trying it). Is there some code that I can use to convert my file into a .dat file so that it can be compatible with qdec? I tried looking through the previous questions and trying some commands (for instance dos2unix -c mac qdec.table.dat, which supposedly replaces LF chars with CR chars). Thanks for your help. Arsenije

2 1

?h.pial_avg in make_average_subject in FS6.0
by Duran, Tugce 12 Dec '17

12 Dec '17

Dear Doug Greve, Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in freesurfer 6.0? Is this file named differently in FS 6.0 or do I need to process this step (where it makes rh or lh.pial_avg) separetely? Thanks, Tugce Duran

2 1

Thalamus and Thalamus-Proper
by 郑凤莲 12 Dec '17

12 Dec '17

Hi FS professors, I am using FS 6.0 for subcortical structures. I have a doubt about thalamus and thalamus-Proper. I added thalamus to brainmask.mgz in Freeview, it shows nothing. However, choose thalamus-Proper, it's ok. I just want to ensure whether the thalamus-Proper in Freesurfer is the same as the thalamus (one of the deep gray matter nuclei) mentioned in other papers. Thank you very much in advance. Sincerely, Zheng

2 1

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by Dijkshoorn, A.B.C. (Aicha) 12 Dec '17

12 Dec '17

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