Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

question about mris_anatomical_stats
by Ali-Reza Mohammadi-Nejad 30 Sep '16

30 Sep '16

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference map is saved in a .mgh file.I think, I can use "mris_anatomical_stats" command for this propose.But, based on the help of this command, I did not find any .mgh file as an input.Therefore, would you please help me to create such stats file?Thank you very much for your help Best regards,Alireza

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How to parcellate the whole white matter into different lobules using Freesurfer ?
by Zhiliang Long 30 Sep '16

30 Sep '16

Dear freesurfer experts: I was wondering if it would be possible to parcellate whole white matter into different lobules (e.g. white matter in frontal lobule, parietal lobule, temporal lobule, and so on) by using Freesurfer ? My goal is to compute the white matter volume, as well as FA wihtin different lobules. Best, Zhiliang

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hello experts
by A-reum Min 30 Sep '16

30 Sep '16

Hello experts. I have some question to you. I used SurfStat statistical tool to analyze the two group(control, patient) When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg. What is the differences between lh.pial and lh.pial_avg ? lh.pial_avg means that real subjects's average pial? plz reply.

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(FSv6 dev) recon-all -base ERROR: segmentation fault
by Duygu Tosun-Turgut 30 Sep '16

30 Sep '16

Hello FreeSurfer Developers, We have been testing a dev version of Freesurfer version 6 (freesurfer-Linux-centos4_x86_64-dev-20160405) Cross-section runs were successful without any error but we have been getting a segmentation fault error while trying to generate the base image for longitudinal processing. The recon-all.log from base image generation run is attached. The command line used is: recon-all -base ABE4869G-1307-base -tp ABE4869G-1307-1 -tp ABE4869G-1307-2 -tp ABE4869G-1307-3 -tp ABE4869G-1307-4 -all Is there a change in the syntax in version 6? or is this a bug in the dev version we have been testing? Thank you

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Can I change the pial surface outline by the adding the control point?
by Seung Gul Kang 30 Sep '16

30 Sep '16

Hi Freesurfer expert, I am doing visual editing. In some subjects, the pial surface border is somewhat narrow (within the border of graymatter in my view) although there is no skull stripping error. I heard that adding the control point might extend the border of graymatter as well as that of white matter from other researcher. Is it true? Or, is there other way to edit to extend the pial surface border? Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ᐧ

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Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
by GAJENDRA KATUWAL (RIT Student) 30 Sep '16

30 Sep '16

Hello FreeSurfer experts, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range (* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by *Katyucia de Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, Marie Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla Zöllei, * it has been mentioned that "Furthermore, we are also planning on making an atlas generated from our training data sets available to the scientific community (as part of the FreeSurfer package), which can serve as a template in structural and functional studies and as a teaching tool for trainees." Has the pediatric template been released yet? Is there anyway the pediatric template can be accessed if it has been released? Is it available in the dev version or upcoming Freesurfer 6? Regards, Gajendra Jung Katuwal PhD Candidate in Imaging Science

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[Philips 3T MRI protocol Recommendation for FreeSurfer]
by 김정식 30 Sep '16

30 Sep '16

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Demeaning of "group" covariate in LME models
by Valsasina Paola 30 Sep '16

30 Sep '16

Dear all, I am trying to perform a longitudinal statistic by using the LME mass univariate toolbox. I have two groups of subjects (each acquired 3 or 4 times over the follow-up), and I want to test whether atrophy progresses differently over time in these two groups. I followed the tutorial on the Website, and I used the following design matrix to test the time x group interaction: X=[ones(length (M),1) M M(:,1).*M(:,2)] I first tried to code the categorical variable "group" assigning values 1 and 2 for subjects belonging to group 1 and 2, respectively (as it is suggested also in the tutorial). Then, I tried to re-run the same model by using mean-centered values for "group" (i.e., assigning -1 to subjects of group 1, and 1 to subjects of group 2). When I run the two statistical models, I obtain different results. Therefore, I would like to ask which is the correct way to model the group covariate? Should it be zero-centered or not? How de-meaning is affecting the estimate? Thank you so much for any suggestion Kind regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all'Ospedale San Raffaele: perch? al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c'? cura, senza ricerca. Non c'? ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg]

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Projecting processed 4D functional data to individual surfaces
by Jared Zimmerman 29 Sep '16

29 Sep '16

Hi All, I'm trying to project some processed resting-state data onto the surface to run some surface based parcellations, and I'm running into a bit of difficulty. Basically I'm using bbregister to register my functional to the T1, then mri_vol2surf to project to the surface with the following pseudocode: bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \ --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \ --init-fsl --bold mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \ --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \ --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape The registration looks pretty good after I run bbregister, but what I get out from the mri_vol2surf seems weird. First of all, the dimensions are 112745 x 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it seems like the x-dim should be 40962 for icoorder=6. I have 120 frames in my input data, so that seems to be right, but I'm not sure where this dimension is coming from. I've also tried it with icoorder=4 and I get the same x-dim=112745 when I'm expecting 2562. I've also run these commands with various iterations e.g. reshaping, no smoothing, no projfrac, and I get the same thing every time. I'm also wondering how I should view these files to confirm that the surface projection has worked as I expect it if/when I am able to get the dimensions to be correct. I cannot open any of the projected functional files in either freeview or tksurfer, so it will be helpful to know how I might be able to view these time-series on the surface after I've succeeded in projecting them to that space. Any advice would be much appreciated Thanks, Jared

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Re: [Freesurfer] Infalted/Label
by Bruce Fischl 29 Sep '16

29 Sep '16

I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote: > Hi, > > I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong? > > Thank you, > Anna > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:00 PM > To: Crawford, Anna > Cc: Anna Crawford; Douglas N. Greve > Subject: RE: Infalted/Label > > Hi Anna > > the label you send me hasn't been sampled onto the surface, which is why > it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You > can tell this is the case as the first column has all -1. If it had been > sampled onto the surface these values would be in [0, nvertices]. > > Does you newer one have non-zero values in this column? > > cheers > Bruce > > On Thu, 29 Sep 2016, > Crawford, Anna wrote: > >> It is in the left hemisphere. >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 10:38 AM >> To: Anna Crawford >> Cc: Crawford, Anna; Douglas N. Greve >> Subject: Re: Infalted/Label >> >> are the labels lh or rh? >> On Wed, 28 Sep 2016, Anna Crawford wrote: >> >>> Hopefully this works better for you. Thank you, >>> >>> Anna >>> >>> >> >> >> 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. >> >> >> =================================== >> >> >> 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. >> >> >> > > =================================== > > > 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. > > >

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