Freesurfer

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30070 discussions

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

2 3

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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recon-all on T1s without anterior coil
by Gullickson, James 12 Jun '17

12 Jun '17

Hello all, We have a subject whose T1s were collected without the anterior head coil engaged, due to a technical error. The posterior coil collected signal. This was on a Siemens Prisma 3T scanner. Would you expect Freesurfer to still be able to process/segment this data accurately, or is it a lost cause at this point? Thanks, James Gullickson

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Re: [Freesurfer] Outputs from 5.3 to 6.0
by Antonin Skoch 12 Jun '17

12 Jun '17

Dear Manuel, I would chime in with my current experience with transfering v5.3 reconstructions to v6.0: The wm segmentation results (and therefore white/pial surfaces, apart from other things) are different between versions, especially in ambiguous areas and especially if there is a difference in interpolation during conform step (in v 6.0 the cubic interpolation is off; if it is off or on in v5.3 it depends on whether you used patched version of recon-all or not). It of course also depends on the quality of your data. In any case, my experience is, if you want to keep high quality of your results, you probably would need to re-inspect your data again and correct newly appeared errors in surfaces. Antonin Skoch all the edits will be taken into account regardless of what command line args you use On 6/9/17 3:08 AM, Manuel Delgado wrote: Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel

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