Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5
by Elijah Mak 14 Jun '17

14 Jun '17

Hi Freesurfer Team, Is there a way to visualise the sampling edges across a range of projfrac values (0.1 (closer to WM) - 0.5) and overlay them onto PET data? Any suggestions are greatly appreciated. Thanks. Best Wishes, Elijah

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Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis
by Tamara Tavares 13 Jun '17

13 Jun '17

Thank you Douglas. For some reason your response was sent in a link to my first post but not the second... I will be looking at the ventricular volume and cortical thickness separately for two different studies. Should the data be smoothed to look at ventricular volume and cortical thickness or just cortical thickness? Also, Does Qdec need to be used to complete the analysis, or can I export the data into another statistical software? Thank you in advance. Best, Tamara Message: 4 Date: Fri, 9 Jun 2017 12:47:06 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0689d6d2-1a15-f5f7-04d1-43e518625899(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed here it is again. The responses are embedded On 06/09/2017 09:51 AM, Douglas Greve wrote: > >The data does not necessarily need to be smoothed, but people usually do because it improves stats. But I thought you were doing an ROI analysis based on the first question<br> > > On 6/6/17 11:50 AM, Tamara Tavares wrote: >> Hello, >> >> I have ran my data through the default recon-all processing stream >> and am planning on analyzing ventricular volume and cortical >> thickness. I was wondering whether I need to use the Qdec to complete >> the ventricular volume and cortical thickness analysis, or can I >> export the data (txt files found in the stats folder) and complete >> the analysis on any statistical program such as SPSS or STATA? > you can export >> >> I also noticed that Qdec needs to have the data smoothed before >> analyzing cortical thickness or other surface information. Why does >> the data need to be smoothed after being ran through recon-all and >> before analysis? Does the smoothing just need to occur if I am >> running the analysis via Qdec or do I need to complete the smoothing >> before analyzing the data on any statistical program? > The data does not necessarily need to be smoothed, but people usually > do because it improves stats. But I thought you were doing an ROI > analysis based on the first question >> >> Thank you in advance for your help! >> >> Best, >> Tamara

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Retrieving Model R^2 From FSFAST GLM Output?
by Taylor, Johnmark 13 Jun '17

13 Jun '17

Hello, Is there a simple way to retrieve the R^2 of the GLM model fit for each voxel from the output of FSFAST? I wonder if rho1.nii.gz might be relevant, but I couldn't find any documentation on this particular file. Thank you very much, JohnMark

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mris_label2nnot
by Almarshad F. 13 Jun '17

13 Jun '17

Hi FreeSurfer team; i'm having diffuculty in creating the annotation file.. i had put all the labels i need to use the file and equal_parcellation_lh, and prepared my LUtable.txt .. when i run the command mris_label2annot it creates an empty annot file with 0 labels .. below is the command and its result .. mris_label2annot --s NMI --h lh --no-unknown --ctab NMI/label/equal_parcellation_lh/mylut.txt --a laparc --ldir NMI/label/equal_parcellation_lh Reading ctab NMI/label/equal_parcellation_lh/mylut.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs cmdline mris_label2annot --s NMI --h lh --no-unknown --ctab NMI/label/equal_parcellation_lh/mylut.txt --a laparc --ldir NMI/label/equal_parcellation_lh sysname Linux hostname fatima-DQ67SW machine x86_64 user fatima subject NMI hemi lh SUBJECTS_DIR /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs ColorTable NMI/label/equal_parcellation_lh/mylut.txt AnnotName laparc nlables 0 LabelThresh 0 0.000000 Loading /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs/NMI/surf/lh.orig Writing annot to /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs/NMI/label/lh.laparc.annot any help will be much appreciated regards; Fatima

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The sulc file from mris_inflate
by Reza Rajimehr 12 Jun '17

12 Jun '17

Hi, We have used mris_inflate: mris_inflate rh.smoothwm rh.inflated The command generates inflated and sulc files. We would like to do a little bit of smoothing on the sulc file, so that we get rid of few scattered regions where small positive curvature islands are located within negative curvature areas (and vice versa). How can we achieve this? mris_inflate has two options: -n and -dist, but assigning different values for these options doesn't seem to have any effects. Thanks, Reza

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Multi-session alignment of functional .nii.gz to single orig.mgz
by Rademaker, Rosanne 12 Jun '17

12 Jun '17

Hi FreeSurfer team, I am running a 3 day experiment and want to concatenate my data in time. Thus, I’ve been trying to transform my data such that voxel indices from all my sessions/days line up (subject’s head is in the scanner slightly differently on each day). First, I created a 3D Motion Correction template for each day (i.e. MCTemplate1.nii.gz, MCTemplate2.nii.gz, MCTemplate3.nii.gz) and aligned each template to a FreeSurfer orig.mgz manually (because the anatomy comes from a different session): tkregister2 --s bert --mov MCTemplate1.nii.gz --regheader-center --reg manreg_day1.dat Then I used bbregister for finetuning the alignment bbregister: bbregister --s bert --mov MCTemplate1.nii.gz --reg autoreg_day1.dat --init-reg manreg_day1.dat --bold --o bboutput_day1.nii.gz So I end up with 3 registration matrices (.dat) that map between the 3 functional volumes and the 1 anatomy. I also have 3 nifti files of the functional volumes that have been resampled into the anatomical space. When I open these in fslview (open one, add the others) they are all aligned and sharing voxel indices as I want, but they are also oriented wrongly, and too big (for the sake of analysis speed later on I want to keep functional data in its original size). The same nifti's output with the --no-resample flag do not overlay once viewed with fslview. I could describe all the other things I have tried but that would make this a very long message (i.e. saving out the regheader matrices and concatenating with those, inverting the transformations and using flirt to apply those, etc. etc.). My hope is someone has figured this out before and could tell me the correct steps. Pointers would be much appreciated! -Rosanne

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leaving out one timepoint from a longitudinal analysis
by Valsasina Paola 12 Jun '17

12 Jun '17

Dear all I already ran the Freesurfer longitudinal stream on 4 timepoints from a set of subjects (dataset1). I would like to perform a new analysis, merging these subjects with another subjects' dataset (dataset2), which has only 3 timepoints. For this second analysis, I will use just the first 3 timepoints of dataset1. Should I re-run the longitudinal stream on the first 3 timepoints of dataset1, or is it fine if I use the output I already have (obtained using a template with 4 timepoints)? Thanks for any suggestion Best regards Paola [BannerOSR_731X129-01]<http://www.5xmille.org/> 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 Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail.

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Re: [Freesurfer] LME correction in longitudinal analysis
by Livia Liu 12 Jun '17

12 Jun '17

Dear FS experts, I want to add some in my early mail. If the contrast CM.C= [0 0 0 1] is designed for the interaction effect(time and group). How to design contrasts to do the main effect about the time and group? CM.C=[0 1 0 1] and CM.C=[0 0 1 1]? Or other? I wonder I may be wrong in designing matrix X in early mail. Please help me.Looking forward to reply, and thanks very much. Kind regards, Livia

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TRACULA -path issue
by Simon, Katrina R 12 Jun '17

12 Jun '17

Hi all, I am running TRACULA on free surfer 6.0.0 and have done the 1st and 2nd step and am getting stuck on the last step with the following error. Loading atlas reference volume from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz niiRead(): error opening file /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux This file is not in the dlabel/mni folder- is this because of something going wrong in the 1st and 2nd steps? Or could it be a problem with loading the atlas reference volume? I have tried this with multiple subjects and am getting the same issue for each one. Any help would be appreciated. Thanks, Katrina Katrina Simon Research Specialist- Mackey Lab University of Pennsylvania Department of Psychology katsimon(a)sas.upenn.edu<mailto:katsimon@sas.upenn.edu> (215) 573-1670

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Difference between -autorecon2-wm and -autorecon2-noaseg ?
by Makaretz, Sara Johanna 12 Jun '17

12 Jun '17

Hi, I'm using FS v6.0 stable. Is there any difference between running recon-all with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at -normalization2 and running through the rest of autorecon2 with no changes to inputs/args compared to "regular" -autorecon2. Is this true, and can I use -autorecon2-wm and -autorecon2-noaseg interchangeably? https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 Thanks! Sara

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Freesurfer June 2017