Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Fwd: Creare Annot File in Freesurface
by Faeze Vedaei 24 Feb '16

24 Feb '16

Hil Freesurfer experts, I am trying to create annot file in freesurface using mris_label2annot command. In this process, I got an error : cannot find or read 'labelfile'sname.label'. I want to help me and explain what is the problem I have such this error for every label file I practice? Here is the command line I used : mris_label2annot --s 002_S_0295 --h lh --ctab 002_S_0295/LABELS/aparc.annot.a2009s.ctab --a myaparc --l lh.G_orbital.label ERROR: cannot find or read lh.G_orbital.label. I'd appreciate it if you clarify me about this process and how I can solve this. Regards, Faezeh Vedaei

2 1

bbregister problems
by Pradeep 24 Feb '16

24 Feb '16

Hello All, I am trying to map pet scans to MRI using bbregister and quite a few subjects were improperly registered. Here are my steps: bbregister --s $fs --mov ${pet_ext}_LIA.nii --init-fsl --t1 --lta output.lta tkregister2 --mov summed_LIA.nii --reg output.dat --surf [ mri]$ more output.dat.mincost 0.860663 0.000513 0.000492 -11.863233 The first value is quite close to 1 so its bad I have attached a screen shot of the image and the log file generated after bbregister. Please let me know if there are any parameters that I could tweak to make the registration better. Thank you for your help, -Pradeep

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Re: [Freesurfer] [Fsdev] [PATCH] fix ups for DESTDIR
by Z K 23 Feb '16

23 Feb '16

Hello Yaroslav, It the case when "some subdirs makefiles do not care about DESTDIR, which is generally respected by autotools" an autotools version issue? Or related to something else completely? I see that making the change on my end does not produce any ill effects, but I would like to observe the behavior before committing the "fix". -Zeke On 02/22/2016 11:33 PM, Yaroslav Halchenko wrote: > Dear FS Developers, > > Per ZK's blessing I am moving my "whining"... khe khe... dialogue over > to fsdev mailing list. And would like to begin with this patch which > have got buried in the users' mailing list: > > I have got into a problem that currently some subdirs makefiles do not > care about DESTDIR, which is generally respected by autotools... > attached patch should help to make FS 'installable' e.g. via > > make install DESTDIR=$PWD/INSTALL-DIR/ > > NB in the future, it would be a nice "test" to add to .travis.yml > upon successful build, without system wide installation with sudo ;) > > Please review/adopt/accept. > > With best regards, > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > _______________________________________________ > Fsdev mailing list > Fsdev(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev >

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FreeSurfer group analysis: mri_glmfit-sim
by Silas 23 Feb '16

23 Feb '16

Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas

2 5

Convert spm volume to fresurfer surface
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Fresurfer users, I would like to analyze group differences in cortical thickness in fresurfer by using as a mask a volumetric SPM activity image. Which command should be used for this purpose? Thanks a lot and best wishes, Sofia

3 2

Still age corrected?
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Freesurfer user, We have performed group contrasts on cortical thickness correcting by age. Now we want to use the mean cortical thickness of one of the significant clusters as a regressor in other analysis, but we do not know whether the mean cortical thickness value for each subject within this ROI is corrected by age or not. Best regards and thank you

3 2

Regarding: 1.5T images
by Dr Sampada Sinha 23 Feb '16

23 Feb '16

Hello freesurfer experts, I am trying to do T1w analysis using freesurfer. The raw images are in dicom format. However, when I view those raw dicom images, some of the brain areas are missing. I just wanted to ask if there is any tool to reconstruct those missing brain areas in the raw images using freesurfer or I need to discard those participants scan altogether? Also, because the resolution is not good with 1.5T, I have seen that skull stripping is not good with a large chunk of skull tissue coming in the processed images. I tried to adjust the watershed parameters and somehow it worked, but it wasn't satisfactory. I tried to run it through fsl bet and got a good skull strip. However, after running the recon-all followed by auorecon11 no skull strip command the with autorecon2 and autorecon3 I am getting excessive topologic defect. I am attaching the log file with this email for your perusal Will greatly appreciate if I can be helped regarding these two problems I am presently facing with the analysis. Thanks and regards, Sampada Pre-doctoral student India

2 1

control points function
by Kiersten Snyder 23 Feb '16

23 Feb '16

Hello, I am new to using Freesurfer and am currently using it for a biomedical image processing class. I am working on a project and would like to know the image processing technique behind the Control Points function. Is it region growing, or what other process? Thanks for the help! Kiersten

2 1

Ris: eTIV question
by angela.favaro＠unipd.it 23 Feb '16

23 Feb '16

3 6

Read_surf error in reading "lh.seghead" head surface created from "mkheadsurf"
by Maheen Siddiqui 22 Feb '16

22 Feb '16

Dear FreeSurfer users, I have used the "mkheadsurf" function to create "lh.seghead" in the surf folder of my subject. Now I am trying to extract the vertices and faces of "lh.seghead" in the following way: *[vertex_coords, faces] = read_surf('lh.seghead')* but get an error in read_surf which is: *Undefined function or variable "faces".* * Error in read_surf (line 80)* * faces = faces+1;* After a bit of investigation I found that the "magic" number of the file is 16777213 while the triangle magic number is 16777214. Since these are unequal, it doesn't go into the if statement where faces are defined. When I try to changed the magic number manually to be the same as the triangle magic number, I get the following error: *Error using reshape* * To RESHAPE the number of elements must not change.* * Error in read_surf (line 76)* * faces = reshape(faces, 3, fnum)' ;* But I don't think making this change is a good idea as it would affect the surfaces that I try to read that DO have magic number that is actually equal to the triangle magic number. Does anybody know why this might be happening? Any suggestions for me to try? The read_surf works fine when I use it for the pial surface, just not the lh.seghead. I am using FreeSurfer version 5.3.0. I would appreciate any advice! Thanks, Maheen

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Freesurfer February 2016