Freesurfer

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17 participants
30099 discussions

Comparison of surface and euclidean distances of fsaverage
by pfannmoelj＠uni-greifswald.de 08 Oct '14

08 Oct '14

Dear FreeSurfer experts, I computed distances on the cortex surface of fsaverage using mris_pmake. The exact syntax of the distance computation was: mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:XXXXX,endVertex:XXXXX . Subsequently, the euclidean distance was computed using the MNI coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startMNI_x-stopMNI_x)^2+(startMNI_y-stopMNI_y)^2+(startMNI_z-stopMNI_z)^2] . The in-surface distance must be larger or equal to the euclidean distance. However, in ~50% of the cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution? How can it be corrected? I am using FreeSurfer 5.3 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely yours pfannmoe

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Gyrification index vs cortical surface area
by Knut J Bjuland 07 Oct '14

07 Oct '14

Dear FreeSurfer experts I have run analyses on gyrification index. I was wondering if anybody could tell me what exactly is the relationship between gyrification index and cortical area. My gyrification results and area results are to a large extent similar. Am I measuring approximately the same thing? Thank you Knut Jørgen Bjuland PhD candidate The Norwegian University of Science and Technology (NTNU) Trondheim, Norway

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sequence advice for GE 750 & 8-channel coil
by Antonio Algaze Beato 06 Oct '14

06 Oct '14

Dear Freesurfer users, Greetings from Puerto Rico. I am new to FS and would appreciate it very much if you could share some suggestions on appropriate parameters for a GE 750 3T using an 8-channel coil and running system software v. 23.1. I searched the list for these, but could not find anything relatively recent. Your help will be greatly appreciated. Cheers, Antonio

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Visualizing individual ROI labels
by Elissa McIntosh 06 Oct '14

06 Oct '14

Hello freesurfer experts, I am hoping that someone can tell me how I can create 3D representations of individual cortical ROIs (labels based on the Desikan/Killiany Atlas) to be used in figures. I'm trying to make figures that show the ROIs that I investigated (like this figure in Desikan et al. paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012853) I know that I can manually make a label in qdec, but I was hoping that there was an automated method to highlighting individual labels/ROIs. Thank you, Elissa

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Freesurfer troubleshooting for ageing data
by Niklas Kasenburg 06 Oct '14

06 Oct '14

Hello fellow Freesurfer user, I am currently working on an ageing data set (~60 subjects between 19 to 81 years old). I mainly want to use Freesurfer for two different things: 1. get a cortical and sub-cortical segmentation to use those regions for a connectivity analysis 2. use the WM/GM boundary and the pial surface to compute cortical thickness I have run recon-all -autorecon2 for all subjects based on T1-weighted structural images. I am no in the process of making sure that everything worked before continuing (I already checked after autorecon-1 that the skull striping didn't remove large chunks of the brain). Therefore, I looked at the surfaces and saw that there are problems with almost half of my subjects due to bad skull striping (WM/GM boundary or pial surface extends to skull). I also read that lesions (WM surface cutting into the brain instead of following it) can lead to dimples or holes in the inflated surfaces. I know that one can correct some of those errors manually, but probably not all the errors will have an impact on what I want to use it for. Which brings me to the questions: 1. Which parts are critical for my subsequent analysis (concerning points 1 and 2 above) and therefore need to be corrected? 2. How much time should you generally invest on manual intervention (erasing voxels in brainmask.mgz, filling holes in wm.mgz, etc.) and when should you rather refine parameters in the recon-all processes (see also 3)? 3. If there are a lot of errors due to wrong skull stripping, how can you change steps in the pipeline to improve it? I would really appreciate help with any of the three points, so feel free to just answer to a subset of them. Many thanks in advance! Best regards, Niklas

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excluding labels from analysis
by Adam, Ruth 06 Oct '14

06 Oct '14

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Any ideas on how to automatically measure maximum thickness(diameter) of lesions?
by 조수연 06 Oct '14

06 Oct '14

Hello, dear fellow Freesurfers. I was wondering whether there was any way to automatically measure the longest or the maximum length(or thickness or diameter) of cortical lesions. By this I mean that if there were to say 3 distinctive lesions in the brain of the patient, each with 1mm, 2mm, 7mm maximum diameters, the 7mm will be chosen as the representative "maximum lesion thickness" of the patient. Considering that there are automated methods to measure the average cortical thickness, with a little tweaking, it seems plausible that we can measure the lesion's maximum thickness automatically too. I know there are provided methods that able us to automatically segregate lesion specific areas from T1 FLAIR images. Will there be a way to get the measurements that I want using these masks? Using the masks isn't essential as long as I can get the maximum lesion thickness automatically. I'm not so familiar with computational algorithms so please any form of advice will be appreciated. Thank you for taking your time to read this. Hope all of you have a great day. Sincerely, Sooyun Cho.

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Re: [Freesurfer] White matter and white matter lesions
by Douglas N Greve 06 Oct '14

06 Oct '14

Those are the only WM labels present in the aseg. You may or may not want to include brain stem as WM. On 10/03/2014 04:03 AM, Leise Borg wrote: > > Hi again > > Labels 7 and 46 in the aseg-file gives me the cerebellum white matter > – which I can see from the aseg.stat-file. From the list at > http://www.slicer.org/slicerWiki/index.php/Slicer3:Freesurfer_labels I > can see that I also need the labels 2 and 41. It looks ok to me when I > plot it, but can I be sure that it gives me all white matter (NOT > white matter hypointensities)? I can see that there are several other > labels referring to white matter, such as label 219, 223, 3000 etc. Do > those labels point at subsets of the labels 2 and 41 (and 7 and 46)? > > -Leise > > *From:*Leise Borg > *Sent:* 3. oktober 2014 08:48 > *To:* 'greve(a)nmr.mgh.harvard.edu' > *Subject:* Re: [Freesurfer] White matter and white matter lesions > > Hi Douglas > > Thanks a lot for your answer. I will definitely do that. Can you tell > me how I load this aseg.stats file into Matlab? I do not have > FreeSurfer downloaded on my own computer. Do I need that to load this > file? > > -Leise. > > Why not just use the values in aseg.stats? > > On 10/01/2014 07:44 AM, Leise Borg wrote: > > > > > > Hi FreeSurfer > > > > > > I am working on a project concerning Alzheimer’s patients and I need > > > to know the positions of white matter (WM) and white matter lesions > > > (WML) from your segmentations. > > > > > > To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. > > > > > > To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and > > > subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 > > > found in the aseg.mgz-files. > > > > > > However, in the two sets of positions – one for WML and one for WM > > > –there is an overlap. It is not big, but it is there. > > > > > > Can you help me finding the true WML- and WM-segmentations? > > > > > > With kind regards, Leise. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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PhD position in tractography validation, Inserm U930 "Brain and imaging" lab, University François-Rabelais of Tours
by Frédéric Andersson 06 Oct '14

06 Oct '14

"A funded PhD Student position will be available in the “Brain and Imaging” Inserm unit (national institute for health) settled in Tours, France, from October 1st, 2014 to September 30th, 2017. During this time period, the candidate will have: (1) to develop tools and pertinent criteria for comparison of MR-based tractography results to data obtained from dissection; (2) to compare different algorithms used for MR-based tractography; (3) to develop a tool aiming to help decision making for the choice of optimal algorithms and parameters used for tractography. This work will be co-directed by Pr C Destrieux (Anatomist) and Pr G Venturini (Computer Science) in the university of Tours. It will be funded for the whole time period by a grant we obtained from the Ministry of Research (about 1400 € per month). Potential candidates have to send a letter and a CV to christophe.destrieux(a)univ-tours.fr and gilles.venturini(a)univ-tours.fr before the 15th of April. After an internal selection of the applications, they will have to defend their candidateship during an interview organized by the Doctoral School of the university at the end of May 2014."

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Transform MNI-space segmentation into Subject-space
by Roy Talman 06 Oct '14

06 Oct '14

Hello I have a segmentation which made on MNI space, is it possible to do the inverse transform to the segmentation from MNI space to each subject space? does the size of the MNI segmentation (218*182*182) should be a problam? I was traing : mri_vol2surf MNI_Segmentation.nii --hemi lh --regheader bert --o /home/cnilab/ProgramFiles/freesurfer/NewFileName.mgz but i get a empty file. is there a diffrante way to do this? thanks. roy

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