Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

fieldsign map display
by Francesca Strappini 04 Sep '14

04 Sep '14

Dear all, I'm trying to display the fieldsign map. I used standard rotating-wedge and expanding-ring paradigm, and I followed the steps described in FsFastIndividualRetinotopy Analysis. I'm running freesurfer on Ubuntu 14.04. Polar angle and eccentricity map look good but I can't properly display the fieldsign map as an alternation of two colours. I attached a screen-shot as example. Any suggestion? Thanks for the help! Francesca The command line is; tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign and that's the output: shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy> tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign Surface DM lh Map Surface DM lh $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ Linux shalim-ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 2 17:28:57 IDT 2014 /usr/local/freesurfer/bin/tksurfer list fieldsign con/map fieldsign /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz maplist /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz mri_concat /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz --o /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii cd /usr/local/freesurfer/fsfast/MeytalRetinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer DM lh inflated -overlay /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 0.5 -fmid 2.25000000000000000000 -fslope .28571428571428571428 -mask /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz -mask-thresh 0.5 -fthresh .01 Contrasts 0 fieldsign setting colscalebarflag to 1 setting fthresh to 0.5000 setting fmid to 2.2500 setting fslope to 0.2857 mrismaskfile /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 0.5000 setting fthresh to 0.0100 subject is DM hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/fsfast/MeytalRetinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/DM) Reading /usr/local/freesurfer/subjects/DM/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/DM/mri/orig.mgz surfer: vertices=118099, faces=236194 tkmedit: Trying to open /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii as encoded scalar volume. surfer: curvature read: min=-1.094241 max=1.337460 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8089 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(DM) Reading mris mask /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ^CKilled Area degli allegati Visualizza anteprima allegato fieldsign_map.tiff Fai clic qui per rispondere o inoltrare il messaggio 7,02 GB (46%) di 15 GB utilizzati Gestisci Ultima attività dell'account: 2 minuti fa Dettagli

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Masks based on 10-20 locations of stimulating electrodes
by Tudor Popescu 04 Sep '14

04 Sep '14

Dear FS team, I have structural data from a training study involving different tDCS groups. I would like to define ROIs (masks) in MNI space corresponding to the approximate cortical area underlying the tDCS electrodes, which were placed on F3&F4 for one group and on P3&P4 in another group (10-20 system positions). I would therefore need to find the approximate centre coordinates, in MNI space, for the F3, F4, P3, P4 electrode positions; however, this is proving challenging. Other papers that have done this (1 <http://www.sciencedirect.com/science/article/pii/S0960982213007136>, 2 <http://www.jneurosci.org/content/31/43/15284.short>) have obtained coordinates for their electrodes (other positions than mine, unfortunately) using various types of converters, such as Brainstorm <http://neuroimage.usc.edu/neuro/BrainStorm>, Comet <http://cone.hanyang.ac.kr/BioEST/Kor/Comets.html>and the Muenster T2T Converter <http://wwwneuro03.uni-muenster.de/ger/t2tconv/conv3d.html>. However, it's proving very time-costly to get any of these to actually produce MNI coordinates at the cortical (not scalp) level for the electrode positions I mentioned. I suppose a scalp-to-cortex projection would have to be done, but I'm still working out how to do it. Clearly many approximations are involved so these won't be very accurate masks, but I want to at least try to define them first. Also, assuming I find the centre coordinates, how would a surface-based mask, of a certain cortical depth and centred around those coordinates, be created in Freesurfer? Many thanks! Best wishes, Tudor

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Vertex space
by lorenzo pasquini 04 Sep '14

04 Sep '14

Dear Freesurfer users, I was wondering if it is possible to transform functional connectivity images (.img format) derived e.g. from an ICA of resting state fMRI data into vertex space reflecting cortical thickness (derived from the Freesurfer pipeline on anatomical data). We have been trying hard with commands as mrivol2surface and bbregister without much success. Do you have any suggestions why it is not working? Can a correspondence of activity and structure be implemented in Freesurfer only if the activation maps are derived from the freesurfer pipeline? Any help is welcome! Cheers, Lorenzo

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Something wrong with fsaverage folder
by Minjeong Wang 04 Sep '14

04 Sep '14

Deal all I have some problem with my fsaverage folder. can i re-download this folder?? or do I need to download the whole freesurfer package again? my freesurfer version is ' freesurfer-i386-apple-darwin11.4.2-stable5-20130514'. Thank you. Sincerely Wang

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Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 04 Sep '14

04 Sep '14

Hi Barbara and FS-community, I tried everything you suggested, but unfortunately the same error still occurs. Have you found a solution yet? Thanks for your help Best regards, Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be Hi Robby, Try this (with the backslashes), applied only to bveclist, if that does not work, also to subjlist and dcmlist at the same time, and let me know please. I have started to process my data with a separate configuration file for every subject :( - as no combination of alterations to the multiple subject configuration file helped me. Maybe you are luckier though. And I am still not sure if there is another way to solve the issue... Thanks, Barbara set bveclist = ( INP_080_LISA_V_1/bvec.txt \ INP_091_KIVA_V_1/bvec.txt \INP_092_LACH_V_1/bvec.txt \ INP_097_LADH_V_1/bvec.txt \WAD_090_MASU_V_1/bvec.txt \ WAD_IWT047_KIMO/bvec.txt \ WAD_IWT043_NAME/bvec.txt \ WAD_IWT021_ALAS/bvec.txt \ WAD_057_PACA/bvec.txt \ WAD_047_JESE/bvec.txt \ WAD_019_NADE/bvec.txt \ WAD_017_CACO/bvec.txt \ INP_IWT046_KATU/bvec.txt \INP_IWT045_INDE/bvec.txt \ INP_IWT007_CIHA/bvec.txt \ INP_IWT001_MOTA/bvec.txt \ INP_082_JAPA/bvec.txt \ INP_081_ELBA/bvec.txt \ INP_079_STEVA/bvec.txt \ INP_063_STCO/bvec.txt \ INP_059_CABR/bvec.txt \ INP_058_NEVA/bvec.txt \ INP_054_LUSO/bvec.txt \ INP_045_ELDA/bvec.txt \ INP_028_JEVE/bvec.txt \ INP_024_LUDE/bvec.txt \ INP_012_JAGU/bvec.txt \ GEZ_078_HEVA/bvec.txt \ GEZ_075_ISKL/bvec.txt \ GEZ_074_FIOR/bvec.txt \ GEZ_049_ELWE/bvec.txt \ GEZ_042_MADE/bvec.txt \ GEZ_038_LIDA/bvec.txt \ GEZ_033_LOVE/bvec.txt \ GEZ_014_GRBU/bvec.txt \ GEZ_006_ELDE/bvec.txt \ GEZ_004_HACO/bvec.txt )

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how generate a head model?
by gamaliel huerta urrea 03 Sep '14

03 Sep '14

Hi Experts I have been studying how to generate a head model, and is said to FreeSurfer software allows better tissue segmentation. I've driven German Gomez Herrero tutorial: http://www.germangh.com/tutorials/dipoles/head_model.htm I have installed freesurfer and matlab. I have verified that the initial elements to generate the model head is MRIs, which have them. I have also verified that using FreeSurfer for segmentation and reconstruction MNE to generate the following areas: 0003-inner_skull-5120.tri 0003-inner_skull-dense.tri 0003-outer_skin-5120.tri 0003-outer_skin-dense.tri 0003-outer_skull-5120.tri 0003-outer_skull-dense.tri My idea is to get the same files to generate my own models and then simulate them power over dipole sources. >From what I have researched the role mri_make_bem_surfaces segmented surfaces, but I only found this material: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_make_bem_surfaces Any help on how to achieve the above-named areas would contribute. Thank you Regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

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prefrontal gyrification
by melinda dora 03 Sep '14

03 Sep '14

Dear list, how would I get gyrification for the prefrotnal cortex? there is no annotation for this structure? Do I need to make my own? and if so, how? best, Melly

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mkanalysis-sess blocked design
by Milde, Christopher 03 Sep '14

03 Sep '14

Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for condition and fixation? I'm using Freesurfer 5.3 Thanks in advance, Chris

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Group cortical thickness QDEC help
by Taylor North 02 Sep '14

02 Sep '14

Hello, I am having some troubles using QDEC to analyze the thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

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Job offer: 1 PhD and 1 PostDoc in Neuroimaging of Epilepsy - Tübingen, Germany
by Niels Focke 02 Sep '14

02 Sep '14

We currently have two open job opportunities at the University of Tübingen, Germany. Both in the field of neuroimaging in epilepsy. 1) PostDoc to work on post-processing of functional and structural MRI / network analysis (graph-theory, classification algorithms, EEG-fMRI) 2) PhD-Student to work on structural post-processing using multispectral MRI and automated lesion detection Details can be found on: http://www.hih-tuebingen.de/stellenangebote/stellenangebote-fuer-wissenschaf tler/translational-neuroimaging-ag-focke Short-URL: http://goo.gl/bA5h1D __________________________________________________________________________ Dr. Niels Focke Oberarzt Abt. Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen AG Translationale Bildgebung Hertie Institut für Klinische Hirnforschung Werner Reichhardt Centre for Integrative Neuroscience

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Freesurfer September 2014