Freesurfer

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30099 discussions

annotation files for cortical labels?
by pavitrak＠nmr.mgh.harvard.edu 01 Jul '14

01 Jul '14

Hi Freesurfer Team, I'd like to view a multicolored quilt of individual cortical icosahedron subdivisions. I have labels for these subdivisions stored in the SUBJECT/label folder I can also batch load all these labels and view them in Freeview but am not sure how to randomize their colors for a multicolored appearance. I looked up how to use annotation files and tried to amalgate all left cortical labels in the SUBJECT/label/ folder as below: - cd $SUBJECTS_DIR/$SUBJECT/label - mris_label2annot --s $SUBJECT --h lh --a leftall.annot But it asks for a color table file - it seems like editing the Freesurfer color table file will be quite involved. I have all the labels data and vertices in a w-file - can I use it to somehow create the colortable that I need, or the annotation file itself? Is this the correct way for my goal? Thank you. Best Regards Pavitra

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Optseq2 Help!!
by Elise Cardinale 01 Jul '14

01 Jul '14

Hello! I am trying to use optseq to optimize my study design and cannot get it to accept the parameters I need for my task and I have officially stumped those helping me at my institution so I need your help! I am trying to run a very simple design where my stimuli are presented for 3.5 seconds and I have 60 stimuli: 10 Montreal Pain 10 Montreal Neutral 10 Ekman Neutral 10 Ekman Fear 10 Ekman Anger 5 Montreal Anger 5 Montreal Fear I calculated that at 3.5 seconds each that equals a total of 210 seconds of task and I added 40 seconds of null (~20% of task). Totaling to 250 seconds. My TR is 2.5 seconds giving me 100 time points. I tried to run the following Optseq command: optseq2 --ntp 100 --tr 2.5 --tprescan 0 --psdwin 0 16 .5 --ev angerE 3.5 10 --ev fearE 3.5 10 --ev angerM 3.5 5 --ev fearM 3.5 5 --ev neutralE 3.5 10 --ev neutralM 3.5 10 --ev pain 3.5 10 --nsearch 10000 --nkeep 6 --o EmotionalFaces_Donor_FINAL2 When I do I get the following: INFO: Setting srand48() seed to 374226 optseq2 $Id: optseq2.c,v 2.15 2009/05/26 18:13:45 greve Exp $ NoSearch = 0 nSearch = 10000 nKeep = 6 PctUpdate = 10.000000 nCB1Opt = 0 seed = 374226 Ntp = 100 TR = 2.5 TPreScan = 0 PSD Window = 0 16 0.5 nEvTypes = 7 EvNo Label Duration nRepsNom 1 angerE 3.500 10 2 fearE 3.500 10 3 angerE 3.500 5 4 fearE 3.500 5 5 neutralE 3.500 10 6 neutralM 3.500 10 7 pain 3.500 10 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = -1 tNullMax = -1 tNullMin = 0 outstem = EmotionalFaces_Donor_FINAL2 AR1 = 0 No refractory penalty Cost = eff OutStem = EmotionalFaces_Donor_FINAL2 Summary File = EmotionalFaces_Donor_FINAL2.sum nTaskAvgs = 224 ERROR: DOF Constraint Violation: number of estimates (224) is greater than or equal to the number of time points (100). To fix: (1) increase the number of time points to 225, or (2) decrease the number of event types, or, (3) reduce the size of the PSD window, or (4) increase the dPSD. If I decrease the PDS window it comes back with 10000/10000 being unusable. I can't change my dPSD interval as my TR is 2.5 and my event is 3.5 and even if I increase my time points (which is not an option- I cannot double the length of my task) it still comes back as 10000/10000 being unusable. Any advice on how to fix this? Thank you so much! -Elise Cardinale --- Laboratory on Social and Affective Neuroscience Georgetown University White Gravenor Hall 302 email: emc62(a)georgetown.edu phone: 202-687-6853

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Mean diffusuvuty MD
by Alshikho, Mohamad J. 01 Jul '14

01 Jul '14

Hi Fs Experts, In order to calculate the mean diffusivity MD in my DTI data I did the following: 1. For the Eigvals.nii (the output of dt_recon) I used the following command line: fslmaths eigvals -div 3 md.nii 2. mri_vol2vol -mov md.nii --reg register.dat --fstarg -- interp nearest -- o md.anat.mgh 3. mri_segstats --seg $SUBJECTS_DIR/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --seg-erode 2 --i md.anat.mgh --sum md.stats is this correct ? I highly appreciate any suggestions and advices Mohamad

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Pons and midbrain segmentation....
by Gonzalo Rojas Costa 01 Jul '14

01 Jul '14

Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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decompression error of CentOS 6.5
by tulu 01 Jul '14

01 Jul '14

Dear freesurfer experts, I download freesurfer CentOS 6 version and my PC is CentOS 6.5 version. When I decompression it, I get error message: gzip: stdin: invalid compressed data--format violated tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I wonder why I get this error message and how to correct it ? Sincerely JLH

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reading & writing surface files in python
by Alex Kell 30 Jun '14

30 Jun '14

hi freesurfers, i'm looking to read and write freesurfer surface files in python -- like MRIread.m & MRIwrite.m but for surfaces and in python. i'm happy to write the code myself, but it seems like the kind of thing that has been done before and i don't want to reinvent the wheel if i don't have to. i poked around and found pyfsio, which reads but doesn't write surfaces. any suggestions? thanks, alex

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4 groups non-linear effect
by Jacobs H (NP) 30 Jun '14

30 Jun '14

Dear FreeSurfer team, We have processed our T1 data of 4 groups of subjects: controls and patients of varying degrees illness. Now we want to perform : - a F-test to compare the 4 groups (we have one covariate that we want to take into account) - a F test to investigate a differential effect of a blood value across the 4 groups. However, this effect might be non-linear (e.g. inverted U-shape). We have made our fsgd-files, but now we are struggling with the contrast files. Could you help us out on how to create these F-test contrasts? Thanks! Heidi

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Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH))
by Chiu, Bryan (PHTH) 30 Jun '14

30 Jun '14

Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work. -Bryan Date: Fri, 27 Jun 2014 17:59:37 +0000 From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Subject: [Freesurfer] recon-all CUDA error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A594981(a)s-itsv-mbx06p.ead.ubc.ca> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows: [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial (http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/) With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan

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Problem with mris_euler_number
by Jürgen Hänggi 30 Jun '14

30 Jun '14

Dear FS experts I am trying to reconstruct surface-based cortical models with a high resolution (0.5x0.5x0.5mm) using the cm flag. After topology fixing, the function mris_euler_number stops and reports the following error: mrisFindNeighbors: ../surf/lh.orig: face[324829].v[2] = 164499, but face 324829 not in vertex 164499 face list Invalid argument Any idea how to fix this problem? Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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how to generate statistics after segmentation of hippocampal subfields
by kangchengwang0808＠gmail.com 28 Jun '14

28 Jun '14

Hi experts, After segmentation of hippocampal subfields, how to generate statistics of the subfield regions, such as volume? Thank you Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China

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