Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

(no subject)
by 林鄞 12 Jul '11

12 Jul '11

Dear everyone, I just have a problem when installing Freesurfer. I can’t process the command of “tkmedit”. How can I solve this problem? Thank you! setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FREESURFER_HOME opt/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh psylab-Lenovo:~> sudo tcsh [sudo] password for psylab: psylab-Lenovo:~# setenv FREESURFER_HOME /usr/local/freesurfer psylab-Lenovo:~# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni psylab-Lenovo:~# sudo tkmedit bert orig.mgz sudo: tkmedit: command not found psylab-Lenovo:~# sudo tcsh psylab-Lenovo:~# tkmedit bert orig.mgz tkmedit: Command not found. psylab-Lenovo:~# apt -get tkmedit apt: Command not found. psylab-Lenovo:~#

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Hippocampal subfield segmentation
by Tricia Merkley 12 Jul '11

12 Jul '11

Hi, I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct? Thanks, Tricia Merkley

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Question about mri_label2label
by John Richey 12 Jul '11

12 Jul '11

Dear freesurfer experts, I have a question about the use of a registration matrix in the context of mri_label2label. I have a series of labels that were created through mri_volcluster (each significant cluster from a .sig map was saved as a uniqe label as a product of that command), and I wish to map each of these from average space (fsaverage) into native space. However, when I use mri_label2label for this purpose some of the clusters map into plausible subject-space, however others are obviously incorrect. Here is the command line that I have used: mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} --trgsubject ${SUBJECT} --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} --regmethod volume --reg $SUBJECTS_DIR/${SUBJECT}/bold/register.dat I have also tried this command without --reg, but no luck. It seems like I would need a registration matrix that maps each subject to fsaverage, no? Thanks very much in advance,

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tkregister2
by Ignacio Letelier 12 Jul '11

12 Jul '11

Hi freesurefers I tried to visualize my functional data using the command: tkregister2 --s --reg --fslreg --surf orig --tag and i received this error : ERROR: trying to convert FSL registration matrix to FreeSurfer, but FSLOUTPUTTYPE variable is not set. Can anyone help me with this , Thanks in advance , best regards. -- Ignacio

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QDEC thickness data to table
by Alexandru Hanganu 12 Jul '11

12 Jul '11

Dear Freesurfer experts, In the QDEC plot there is the possibility to view cortical thickness for each subject in a specific region. Is there a possibility to make an automatic table of all these thickness data ? In a previous question, the answer was to use a script: =========================== # Script created December 2007 by Pedro Paulo Jr. # Use with Freesurfer 4.x # Updated: 24/03/2010 set FSAVERAGE_DIR = "usr/local/freesurfer/subjects/fsaverage" cd /usr/local/freesurfer/subjects/qdec/QDEC-DATA set numsubject = 17 for i in 'seq 1 $numsubject' do mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc done =========================== But that script doesn't work in tcsh, so we changed the cmd line: =========================== foreach i in (`seq 1 $numsubject`) mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc end =========================== But we still receive error. Can you please help us ? (we use FS 5.1, Centos4_x86_64) Thank you in advance, Sincerely, Alex. * *

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mri_convert and orientation
by Yang Liu 12 Jul '11

12 Jul '11

Hi all, I have a nifti file f.nii whose size is 80*80*60*266, (266 is the TRs). Using "mri_info f.nii", I can see that its orientation is is PIL. I want to change it to RPI. I do the following: "mri_conver --in_orientation PIL --out_orientation RPI -i f.nii -o f.rpi.nii" It give me f.rpi.nii, which has an orientaion of RPI. The problem is that f.rpi.nii is 80*80*60. It contains only one volume. How can I get a reoriented volume that has the same size as the original 80*80*60*266? Many thanks. Yang

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New version and workflow
by Myriam Siefert 11 Jul '11

11 Jul '11

Hello Freesurfer users and experts, We already run 55 subjects with Freesurfer 5.0 and wish now to increase our sample size up to 200 and are now deciding whether to run everybody again with Freesurfer 5.1 or just go on with the previous version. We are doing subcortical analysis (amygdala) and hopefully cortical analysis (correlations with behavioural results), on Siemens 3T. I have 2 questions relative to this issue : - To what extend should the results be more accurate or reliable (I read in the release note that 3T data is now better handled) ? I run 3 subjects on boths versions and compared aseg stats, most results were very close except for a few that were highly discrepant (ex left amygdala and hippocampus for 1 subject were much smaller with FS 5.1). What could explain this? - I also noticed on the web site that the recommended workflow had been updated. Is this linked to the new release (if less or no editing is needed, checking the output only after recon-all -all would obviously save time...)? Is less need for editing expected with the new release? Or is less editing now advised ("Less is more")? Thanks in advance for any advice! Myriam Siefert

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Fw: Multiple frames error
by Antonella Kis 11 Jul '11

11 Jul '11

HiBruce, I 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. Thank you for your help! Antonella

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Creation of normalized cortical regions of interest
by 汪贵宏 11 Jul '11

11 Jul '11

Hi,freesurfers: Recently,I read a paper which used freesurfer to processed their data,this is the paper's link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio… In this paper,the antor said : "One of the critical steps of the whole procedure was to partition the participants' cortex into ROIs located in an identical topographic position for each participant despite interindividual anatomical variation. We used Freesurfer to register a labeled mesh from an average brain onto the brain of each individual participant, where each label corresponded to one of 66 anatomical cortical regions . This output provided for every participant a standardized partition of the cortex into 66 regional areas. In a second step, each of these regional areas were subdivided on the Freesurfer average brain into a set of small and compact regions of about 1.5 cm2, resulting in 998 ROIs covering the entire cortex. This subdivision was then registered on the individual brain using the same transformation as for the 66 regional areas thus maintaining the topological constraints of mapping. Consequently, the resulting partitions of the cortex into 66 and 998 ROIs were in anatomically closely matched positions for all participants " So,I wander how can we subdivided the 66 ROIs into 998 ROIs? Thanks, wang

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Nipype 0.4 release
by Chris Filo Gorgolewski 11 Jul '11

11 Jul '11

Dear all, I am delighted to announce release of Nipype version 0.4. Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, Camino, AFNI, Slicer), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. This release brings plenty of improvements. Among the most important are: new modular executions system (direct support for PBS, SGE, and multi-processing), support for Camino, Camino2Trackvis and Connectome Viewer, improved parallel performance of MapNode, and growing collection of ready to use pipelines (have a look at nipype.workflows). Grab it from https://github.com/nipy/nipype/tarball/0.4 For support please use our mailing list: nipy-users(a)googlegroups.com Full changelog: * API: Timestamp hashing does not use ctime anymore. Please update your hashes by running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun * API: Workflow run function no longer supports (inseries, createdirsonly). Functions used in connect string must be pickleable * API: SPM EstimateContrast: ignore_derivs replaced by use_derivs * API: All interfaces: added new config option ignore_exception * API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter cutoff is mandatory (even if its set to np.inf). Additional interfaces SpecifySPMModel and SpecifySparseModel support other types of data. * API: fsl.DTIFit input "save" is now called "save_tensor" * API: All inputs of IdentityInterfaces are mandatory by default. You can turn this off by specifying mandatory_inputs=False to the constructor. * API: fsl FILMGLS input "autocorr_estimate" is now called "autocorr_estimate_only" * API: fsl ContrastMgr now requires access to specific files (no longer accepts the result directory) * API: freesurfer.GLMFit input "surf" is now a boolean with three corresponding inputs -- subject_id, hemi, and surf_geo * ENH: All commandline interfaces display stdout and stderr * ENH: All interfaces raise exceptions on error with an option to suppress * ENH: Supports a plugin interface for execution (current support for multiprocessing, IPython, SGE, PBS) * ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS * ENH: Optionally allows keeping only required outputs * ENH: New interface: utility.Rename to change the name of files, optionally using python string-formatting with inputs or regular expressions matching * ENH: New interface: freesurfer.ApplyMask (mri_mask) * ENH: New FSL interface -- SwapDimensions (fslswapdim) * ENH: Sparse models allow regressor scaling and temporal derivatives * ENH: Added support for the component parts of FSL's TBSS workflow (TBSSSkeleton and DistanceMap) * ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images * ENH: Added several higher-level interfaces to the fslmaths command: - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths * ENH: added support for networx 1.4 and improved iterable expansion * ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines * ENH: Ability to create a hierarchical dot file * ENH: Improved debugging information for rerunning nodes * ENH: Added 'stop_on_first_rerun' option * ENH: Added support for Camino * ENH: Added support for Camino2Trackvis * ENH: Added support for Connectome Viewer * BF: dcm2nii interface handles gzipped files correctly * BF: FNIRT generates proper outputs * BF: fsl.DTIFit now properly collects tensor volume * BF: updatehash now removes old result hash file Enjoy! Chris Gorgolewski on behalf of Team Nipype ( https://www.ohloh.net/p/nipype/contributors )

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